1NCC

CRYSTAL STRUCTURES OF TWO MUTANT NEURAMINIDASE-ANTIBODY COMPLEXES WITH AMINO ACID SUBSTITUTIONS IN THE INTERFACE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Work: 0.212 
  • R-Value Observed: 0.212 

wwPDB Validation 3D Report Full Report



Literature

Crystal structures of two mutant neuraminidase-antibody complexes with amino acid substitutions in the interface.

Tulip, W.R.Varghese, J.N.Webster, R.G.Laver, W.G.Colman, P.M.

(1992) J Mol Biol 227: 149-159

  • DOI: 10.1016/0022-2836(92)90688-g
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The site on influenza virus N9 neuraminidase recognized by NC41 monoclonal antibody comprises 19 amino acid residues that are in direct contact with 17 residues on the antibody. Single sequence changes in some of the neuraminidase residues in the sit ...

    The site on influenza virus N9 neuraminidase recognized by NC41 monoclonal antibody comprises 19 amino acid residues that are in direct contact with 17 residues on the antibody. Single sequence changes in some of the neuraminidase residues in the site markedly reduce antibody binding. However, two mutants have been found within the site, Ile368 to Arg and Asn329 to Asp selected by antibodies other than NC41, and these mutants bind NC41 antibody with only slightly reduced affinity. The three-dimensional structures of the two mutant N9-NC41 antibody complexes as derived from the wild-type complex are presented. Both structures show that some amino acid substitutions can be accommodated within an antigen-antibody interface by local structural rearrangements around the mutation site. In the Ile368 to Arg mutant complex, the side-chain of Arg368 is shifted by 2.9 A from its position in the uncomplexed mutant and a shift of 1.3 A in the position of the light chain residue HisL55 with respect to the wild-type complex is also observed. In the other mutant, the side-chain of Asp329 appears rotated by 150 degrees around C alpha-C beta with respect to the uncomplexed mutant, so that the carboxylate group is moved to the periphery of the antigen-antibody interface. The results provide a basis for understanding some of the potential structural effects of somatic hypermutation on antigen-antibody binding in those cases where the mutation in the antibody occurs at antigen-contacting residues, and demonstrate again the importance of structural context in evaluating the effect of amino acid substitutions on protein structure and function.


    Related Citations: 
    • Refined Crystal Structure of the Influenza Virus N9 Neuraminidase-Nc41 Fab Complex
      Tulip, W.R., Varghese, J.N., Laver, W.G., Webster, R.G., Colman, P.M.
      (1992) J Mol Biol 227: 122
    • Crystal Structures of Neuraminidase-Antibody Complexes
      Tulip, W.R., Varghese, J.N., Webster, R.G., Air, G.M., Laver, W.G., Colman, P.M.
      (1989) Cold Spring Harb Symp Quant Biol 54: 257
    • Three-Dimensional Structure of a Complex of Antibody with Influenza Virus Neuraminidase
      Colman, P.M., Laver, W.G., Varghese, J.N., Baker, A.T., Tulloch, P.A., Air, G.M., Webster, R.G.
      (1987) Nature 326: 358

    Organizational Affiliation

    CSIRO Division of Biomolecular Engineering, Parkville, Victoria, Australia.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
INFLUENZA A SUBTYPE N9 NEURAMINIDASEN389Influenza A virus (A/tern/Australia/G70C/1975(H11N9))Mutation(s): 0 
Gene Names: NA
EC: 3.2.1.18
Find proteins for P03472 (Influenza A virus (strain A/Tern/Australia/G70C/1975 H11N9))
Explore P03472 
Go to UniProtKB:  P03472
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
IGG2A-KAPPA NC41 FAB (LIGHT CHAIN)L214Mus musculusMutation(s): 0 
Protein Feature View
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
IGG2A-KAPPA NC41 FAB (HEAVY CHAIN)H221Mus musculusMutation(s): 0 
Gene Names: Igh-1a
Find proteins for P01865 (Mus musculus)
Explore P01865 
Go to UniProtKB:  P01865
Protein Feature View
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  • Reference Sequence
Oligosaccharides
Entity ID: 4
MoleculeChainsChain Length2D Diagram Glycosylation
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
N
6 N-Glycosylation
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download CCD File 
N
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
CA
Query on CA

Download CCD File 
N
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Work: 0.212 
  • R-Value Observed: 0.212 
  • Space Group: P 4 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 167α = 90
b = 167β = 90
c = 124γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1994-01-31
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Source and taxonomy, Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Database references, Derived calculations, Other, Structure summary